Abstract 3559: Understanding Ewing sarcoma cell fate
Authors: Danh Truong, Sandhya Krishnan, Alexandar Lazar, David McCall, Joseph A. Ludwig
Journal: Cancer Research (2023)

Abstract Like several other translocation-positive sarcomas, Ewing sarcoma (ES) exists exclusively in a high-grade, undifferentiated state. We believe that the pathognomonic EWS-FLI1 fusion protein (FP) responsible for ES is intimately linked to cell fate, differentiation, and plasticity. Over the last two decades, an emerging body of research has begun the challenging task of deciphering how the FP - via its action as an aberrant transcription factor- blocks differentiation and promotes reprogramming toward a quasi-stem-like cell with features of neuroectodermal or mesenchymal stem cells. We compared ES transcriptome data to other cancers in an unsupervised comparison between the gene expression profile of cancer cells in the Cancer Cell Line Encyclopedia (CCLE) and tumor expression datasets. While ES is traditionally classified as a bone cancer, it does not cluster near other bone cancer subtypes (e.g., osteosarcomas) or soft-tissue sarcomas. To that end, we sought to better understand how targeting the FP affected ES differentiation and lineage. Using a CRISPR knockout (CRISPR-KO) model of A673, we targeted Exon 4 of the EWSR1 protein in the n-terminus of the FP and generated a clonal pool (EWSR1 CRISPR KO). We used single-cell RNA sequencing (scRNA-seq) to identify the transcriptional changes after FP knockout (FP KO). We identified five cell clusters in the data. We observed the expression of FP target genes (EWS-FLI1 On), PRKCB, and LIPI and saw robust expression in four of the clusters suggesting normal FP expression. Conversely, FP repressed genes (EWS-FLI1 Off), LOX and IGFBP3, were elevated in cluster 2, which contained only EWSR1 CRISPR KO cells. This suggests that the FP was successfully knocked out in cluster 2 (FP EWSR1 KO). Next, we asked how the FP KO changed the lineage/fate of A673 cells. We hypothesized that loss of the FP would induce mesenchymal/fibroblastic fate in ES cells. To answer this, we used SingleR, which compares the gene expression profile of query cells to the CCLE data set, to identify the nearest cell type. Interestingly, all clusters except the FP EWSR1 KO cluster identified closely with ES and related tumors. The FP EWSR1 KO cluster, which expressed EWS-FLI1 ‘off’ genes, did not resemble ES. Using a granular identification with cell lines, we confirmed that the highest score was A673 since these were A673 cell lines. However, the FP EWSR1 KO resulted in a phenotype unrelated to A673 and more closely resembled cell lines with fibroblastic phenotype. Our data suggest that targeting the FP significantly changed ES lineage. While the FP KO did not lead to cell death, our results suggest a novel gene regulatory network acts to sustain ES lineage. Further perturbations in this network may lead to a better understanding of ES treatment, particularly as novel EWS-FLI1-directed therapies emerge. Citation Format: Danh Truong, Sandhya Krishnan, Alexandar Lazar, David McCall, Joseph A. Ludwig. Understanding Ewing sarcoma cell fate. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3559.